Add UI element for Instrument Settings (#141)

* Add UI element for Instrument Settings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* wow flake is picky

* Add instrument_settings to global settings, some formatting

* add release notes

* fix from_xml for mypy

* add unit test for ui element and model

* line deleted

* working through adding tests

* add loading config tests

* Save instrument settings in XML, some formatting

* change defaults and precision

* fix tests

* Add deprecation warning to SF Calculator

* add test_instrument_settings.xml to test data

* update user docs

* add default settings dict, apply default if not in xml

* convert defaults to dataclass, fix mypy test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Glass

RefRed/about_dialog.py

@@ -8,7 +8,6 @@
 
 
 class AboutDialog(object):
-
     parent = None
 
     def __init__(self, parent=None):
@@ -22,29 +21,20 @@ def display(self):
         qt_version = QT_VERSION
         pyqt_version = PYQT_VERSION
 
-        message = '''RefRed - Liquids Reflectrometry Reduction program
+        message = f"""RefRed - Liquids Reflectrometry Reduction program
 
-        RefRed version %s
-        Reduction version %s
+        RefRed version {RefRed_version_str}
+        Reduction version {lr_reduction.__version__}
 
         Library versions:
-          - Python: %s
-          - Numpy: %s
-          - Mantid:  %s
-          - Matplotlib: %s
-          - Qt: %s
-          - PyQt: %s''' % (
-            RefRed_version_str,
-            lr_reduction.__version__,
-            python_version,
-            numpy_version,
-            mantid_version,
-            matplotlib_version,
-            qt_version,
-            pyqt_version,
-        )
-
-        QtWidgets.QMessageBox.about(self.parent, 'About RefRed', message)
+          - Python: {python_version}
+          - Numpy: {numpy_version}
+          - Mantid:  {mantid_version}
+          - Matplotlib: {matplotlib_version}
+          - Qt: {qt_version}
+          - PyQt: {pyqt_version}"""
+
+        QtWidgets.QMessageBox.about(self.parent, "About RefRed", message)
 
     def get_python_version(self):
         str_version = sys.version_info

RefRed/configuration/export_xml_config.py

@@ -11,7 +11,9 @@
 # package imports
 import RefRed
 from RefRed.calculations.lr_data import LRData
-from RefRed.reduction.global_reduction_settings_handler import GlobalReductionSettingsHandler
+from RefRed.reduction.global_reduction_settings_handler import (
+    GlobalReductionSettingsHandler,
+)
 
 
 class ExportXMLConfig(object):
@@ -21,33 +23,31 @@ def __init__(self, parent=None):
 
     def header_part(self):
         str_array = self.str_array
-        str_array.append('<Reduction>\n')
-        str_array.append(' <instrument_name>REFL</instrument_name>\n')
-        str_array.append(' <timestamp>' + datetime.datetime.now().strftime("%A, %d. %B %Y %I:%M%p") + '</timestamp>\n')
-        str_array.append(' <version>%s</version>\n' % lr_reduction.__version__)
-        str_array.append(' <mantid_version>' + mantid.__version__ + '</mantid_version>\n')
-        str_array.append('<generator>RefRed-%s</generator>\n' % RefRed.__version__)
+        str_array.append("<Reduction>\n")
+        str_array.append(" <instrument_name>REFL</instrument_name>\n")
+        str_array.append(" <timestamp>" + datetime.datetime.now().strftime("%A, %d. %B %Y %I:%M%p") + "</timestamp>\n")
+        str_array.append(" <version>%s</version>\n" % lr_reduction.__version__)
+        str_array.append(" <mantid_version>" + mantid.__version__ + "</mantid_version>\n")
+        str_array.append("<generator>RefRed-%s</generator>\n" % RefRed.__version__)
 
         # metadata
-        str_array.append(' <DataSeries>\n')
+        str_array.append(" <DataSeries>\n")
 
         self.str_array = str_array
 
     def main_part(self):
-
         str_array = self.str_array
         _big_table_data = self.parent.big_table_data
         nbr_row = self.parent.REDUCTIONTABLE_MAX_ROWCOUNT
         o_general_settings = GlobalReductionSettingsHandler(parent=self.parent)
 
         for row in range(nbr_row):
-
             _data: LRData = _big_table_data[row, 0]
             if _data is None:
                 break  # we found the first empty row in the reduction table. No more runs available
 
-            str_array.append('  <RefLData>\n')
-            str_array.append('   <peak_selection_type>narrow</peak_selection_type>\n')
+            str_array.append("  <RefLData>\n")
+            str_array.append("   <peak_selection_type>narrow</peak_selection_type>\n")
 
             data_peak = _data.peak
             data_back = _data.back
@@ -85,79 +85,79 @@ def main_part(self):
                 norm_low_res_flag = False
                 norm_lambda_requested = -1
 
-            str_array.append('   <from_peak_pixels>' + str(data_peak[0]) + '</from_peak_pixels>\n')
-            str_array.append('   <to_peak_pixels>' + str(data_peak[1]) + '</to_peak_pixels>\n')
-            str_array.append('   <peak_discrete_selection>N/A</peak_discrete_selection>\n')
-            str_array.append('   <background_flag>' + str(data_back_flag) + '</background_flag>\n')
-            str_array.append('   <two_backgrounds>' + str(data_two_backgrounds) + '</two_backgrounds>\n')
-            str_array.append('   <back_roi1_from>' + str(data_back[0]) + '</back_roi1_from>\n')
-            str_array.append('   <back_roi1_to>' + str(data_back[1]) + '</back_roi1_to>\n')
-            str_array.append('   <back_roi2_from>' + str(data_back2[0]) + '</back_roi2_from>\n')
-            str_array.append('   <back_roi2_to>' + str(data_back2[1]) + '</back_roi2_to>\n')
-            str_array.append('   <tof_range_flag>True</tof_range_flag>\n')
-            str_array.append('   <from_tof_range>' + str(tof[0]) + '</from_tof_range>\n')
-            str_array.append('   <to_tof_range>' + str(tof[1]) + '</to_tof_range>\n')
-            str_array.append('   <from_q_range>' + str(q_range[0]) + '</from_q_range>\n')
-            str_array.append('   <to_q_range>' + str(q_range[1]) + '</to_q_range>\n')
-            str_array.append('   <from_lambda_range>' + str(lambda_range[0]) + '</from_lambda_range>\n')
-            str_array.append('   <to_lambda_range>' + str(lambda_range[1]) + '</to_lambda_range>\n')
-            str_array.append('   <incident_angle>' + str(incident_angle) + '</incident_angle>\n')
+            str_array.append("   <from_peak_pixels>" + str(data_peak[0]) + "</from_peak_pixels>\n")
+            str_array.append("   <to_peak_pixels>" + str(data_peak[1]) + "</to_peak_pixels>\n")
+            str_array.append("   <peak_discrete_selection>N/A</peak_discrete_selection>\n")
+            str_array.append("   <background_flag>" + str(data_back_flag) + "</background_flag>\n")
+            str_array.append("   <two_backgrounds>" + str(data_two_backgrounds) + "</two_backgrounds>\n")
+            str_array.append("   <back_roi1_from>" + str(data_back[0]) + "</back_roi1_from>\n")
+            str_array.append("   <back_roi1_to>" + str(data_back[1]) + "</back_roi1_to>\n")
+            str_array.append("   <back_roi2_from>" + str(data_back2[0]) + "</back_roi2_from>\n")
+            str_array.append("   <back_roi2_to>" + str(data_back2[1]) + "</back_roi2_to>\n")
+            str_array.append("   <tof_range_flag>True</tof_range_flag>\n")
+            str_array.append("   <from_tof_range>" + str(tof[0]) + "</from_tof_range>\n")
+            str_array.append("   <to_tof_range>" + str(tof[1]) + "</to_tof_range>\n")
+            str_array.append("   <from_q_range>" + str(q_range[0]) + "</from_q_range>\n")
+            str_array.append("   <to_q_range>" + str(q_range[1]) + "</to_q_range>\n")
+            str_array.append("   <from_lambda_range>" + str(lambda_range[0]) + "</from_lambda_range>\n")
+            str_array.append("   <to_lambda_range>" + str(lambda_range[1]) + "</to_lambda_range>\n")
+            str_array.append("   <incident_angle>" + str(incident_angle) + "</incident_angle>\n")
 
             _data_run_number = str(self.parent.ui.reductionTable.item(row, 1).text())
-            str_array.append('   <data_sets>' + _data_run_number + '</data_sets>\n')
+            str_array.append("   <data_sets>" + _data_run_number + "</data_sets>\n")
             # if type(data_full_file_name) == type([]):
             # data_full_file_name = ','.join(data_full_file_name)
             # str_array.append('   <data_full_file_name>' + data_full_file_name + '</data_full_file_name>\n')
 
-            str_array.append('   <x_min_pixel>' + str(data_low_res[0]) + '</x_min_pixel>\n')
-            str_array.append('   <x_max_pixel>' + str(data_low_res[1]) + '</x_max_pixel>\n')
-            str_array.append('   <x_range_flag>' + str(data_low_res_flag) + '</x_range_flag>\n')
+            str_array.append("   <x_min_pixel>" + str(data_low_res[0]) + "</x_min_pixel>\n")
+            str_array.append("   <x_max_pixel>" + str(data_low_res[1]) + "</x_max_pixel>\n")
+            str_array.append("   <x_range_flag>" + str(data_low_res_flag) + "</x_range_flag>\n")
 
             tthd = str(self.parent.ui.metadatatthdValue.text())
-            str_array.append('   <tthd_value>' + tthd + '</tthd_value>\n')
+            str_array.append("   <tthd_value>" + tthd + "</tthd_value>\n")
             ths = str(self.parent.ui.metadatathiValue.text())
-            str_array.append('   <ths_value>' + ths + '</ths_value>\n')
-            str_array.append('   <data_lambda_requested>' + str(data_lambda_requested) + '</data_lambda_requested>\n')
-
-            str_array.append('   <norm_flag>' + str(norm_flag) + '</norm_flag>\n')
-            str_array.append('   <norm_x_range_flag>' + str(norm_low_res_flag) + '</norm_x_range_flag>\n')
-            str_array.append('   <norm_x_max>' + str(norm_low_res[1]) + '</norm_x_max>\n')
-            str_array.append('   <norm_x_min>' + str(norm_low_res[0]) + '</norm_x_min>\n')
-            str_array.append('   <norm_from_peak_pixels>' + str(norm_peak[0]) + '</norm_from_peak_pixels>\n')
-            str_array.append('   <norm_to_peak_pixels>' + str(norm_peak[1]) + '</norm_to_peak_pixels>\n')
-            str_array.append('   <norm_background_flag>' + str(norm_back_flag) + '</norm_background_flag>\n')
-            str_array.append('   <norm_two_backgrounds>' + str(norm_two_backgrounds) + '</norm_two_backgrounds>\n')
-            str_array.append('   <norm_from_back_pixels>' + str(norm_back[0]) + '</norm_from_back_pixels>\n')
-            str_array.append('   <norm_to_back_pixels>' + str(norm_back[1]) + '</norm_to_back_pixels>\n')
-            str_array.append('   <norm_from_back2_pixels>' + str(norm_back2[0]) + '</norm_from_back2_pixels>\n')
-            str_array.append('   <norm_to_back2_pixels>' + str(norm_back2[1]) + '</norm_to_back2_pixels>\n')
-            str_array.append('   <norm_lambda_requested>' + str(norm_lambda_requested) + '</norm_lambda_requested>\n')
+            str_array.append("   <ths_value>" + ths + "</ths_value>\n")
+            str_array.append("   <data_lambda_requested>" + str(data_lambda_requested) + "</data_lambda_requested>\n")
+
+            str_array.append("   <norm_flag>" + str(norm_flag) + "</norm_flag>\n")
+            str_array.append("   <norm_x_range_flag>" + str(norm_low_res_flag) + "</norm_x_range_flag>\n")
+            str_array.append("   <norm_x_max>" + str(norm_low_res[1]) + "</norm_x_max>\n")
+            str_array.append("   <norm_x_min>" + str(norm_low_res[0]) + "</norm_x_min>\n")
+            str_array.append("   <norm_from_peak_pixels>" + str(norm_peak[0]) + "</norm_from_peak_pixels>\n")
+            str_array.append("   <norm_to_peak_pixels>" + str(norm_peak[1]) + "</norm_to_peak_pixels>\n")
+            str_array.append("   <norm_background_flag>" + str(norm_back_flag) + "</norm_background_flag>\n")
+            str_array.append("   <norm_two_backgrounds>" + str(norm_two_backgrounds) + "</norm_two_backgrounds>\n")
+            str_array.append("   <norm_from_back_pixels>" + str(norm_back[0]) + "</norm_from_back_pixels>\n")
+            str_array.append("   <norm_to_back_pixels>" + str(norm_back[1]) + "</norm_to_back_pixels>\n")
+            str_array.append("   <norm_from_back2_pixels>" + str(norm_back2[0]) + "</norm_from_back2_pixels>\n")
+            str_array.append("   <norm_to_back2_pixels>" + str(norm_back2[1]) + "</norm_to_back2_pixels>\n")
+            str_array.append("   <norm_lambda_requested>" + str(norm_lambda_requested) + "</norm_lambda_requested>\n")
 
             _norm_run_number_cell = self.parent.ui.reductionTable.item(row, 2).text()
-            if str(_norm_run_number_cell) != '':
+            if str(_norm_run_number_cell) != "":
                 _norm_run_number = str(_norm_run_number_cell)
             else:
-                _norm_run_number = '0'
-            str_array.append('   <norm_dataset>' + _norm_run_number + '</norm_dataset>\n')
+                _norm_run_number = "0"
+            str_array.append("   <norm_dataset>" + _norm_run_number + "</norm_dataset>\n")
             # if type(norm_full_file_name) == type([]):
             # norm_full_file_name = ','.join(norm_full_file_name)
             # str_array.append('   <norm_full_file_name>' + norm_full_file_name + '</norm_full_file_name>\n')
 
-            str_array.append('   <auto_q_binning>False</auto_q_binning>\n')
+            str_array.append("   <auto_q_binning>False</auto_q_binning>\n")
 
             # The angle offset is currently not exposed in the UI, so we set it to 0.
-            str_array.append('   <angle_offset> 0 </angle_offset>\n')
-            str_array.append('   <angle_offset_error> 0 </angle_offset_error>\n')
+            str_array.append("   <angle_offset> 0 </angle_offset>\n")
+            str_array.append("   <angle_offset_error> 0 </angle_offset_error>\n")
 
             q_step = str(self.parent.ui.qStep.text())
-            str_array.append('   <q_step>' + q_step + '</q_step>\n')
-            q_min = str(self.parent.gui_metadata['q_min'])
-            str_array.append('   <q_min>' + q_min + '</q_min>\n')
+            str_array.append("   <q_step>" + q_step + "</q_step>\n")
+            q_min = str(self.parent.gui_metadata["q_min"])
+            str_array.append("   <q_min>" + q_min + "</q_min>\n")
 
             scalingFactorFlag = self.parent.ui.scalingFactorFlag.isChecked()
-            str_array.append('   <scaling_factor_flag>' + str(scalingFactorFlag) + '</scaling_factor_flag>\n')
+            str_array.append("   <scaling_factor_flag>" + str(scalingFactorFlag) + "</scaling_factor_flag>\n")
             scalingFactorFile = o_general_settings.scaling_factor_file
-            str_array.append('   <scaling_factor_file>' + scalingFactorFile + '</scaling_factor_file>\n')
+            str_array.append("   <scaling_factor_file>" + scalingFactorFile + "</scaling_factor_file>\n")
 
             # incident medium
             allItems = [
@@ -166,23 +166,27 @@ def main_part(self):
             ]
             finalList = allItems[1:]
             strFinalList = ",".join(finalList)
-            str_array.append('   <incident_medium_list>' + strFinalList + '</incident_medium_list>\n')
+            str_array.append("   <incident_medium_list>" + strFinalList + "</incident_medium_list>\n")
 
             imIndex = self.parent.ui.selectIncidentMediumList.currentIndex()
             str_array.append(
-                '   <incident_medium_index_selected>' + str(imIndex - 1) + '</incident_medium_index_selected>\n'
+                "   <incident_medium_index_selected>" + str(imIndex - 1) + "</incident_medium_index_selected>\n"
             )
 
-            str_array.append('   <slits_width_flag>True</slits_width_flag>\n')
+            str_array.append("   <slits_width_flag>True</slits_width_flag>\n")
+
+            # dead time settings
+            str_array.append(o_general_settings.dead_time.to_xml(indent="   ") + "\n")
 
-            str_array.append(o_general_settings.dead_time.to_xml(indent="   ") + "\n")  # dead time settings
+            # instrument settings
+            str_array.append(o_general_settings.instrument_settings.to_xml(indent="   ") + "\n")
 
-            str_array.append('   <const_q>' + str(const_q) + '</const_q>\n')
+            str_array.append("   <const_q>" + str(const_q) + "</const_q>\n")
 
-            str_array.append('  </RefLData>\n')
+            str_array.append("  </RefLData>\n")
 
-        str_array.append('  </DataSeries>\n')
-        str_array.append('</Reduction>\n')
+        str_array.append("  </DataSeries>\n")
+        str_array.append("</Reduction>\n")
         self.str_array = str_array
 
     def save(self, filename: str):
@@ -198,7 +202,7 @@ def save(self, filename: str):
 
         if os.path.isfile(filename):
             os.remove(filename)
-        with open(filename, 'w') as outfile:
+        with open(filename, "w") as outfile:
             outfile.writelines(self.str_array)
 
         logging.info(f"Config is saved to {filename}.")

RefRed/configuration/load_reduction_table_from_lconfigdataset.py

@@ -1,12 +1,15 @@
 from qtpy import QtGui, QtWidgets
+
+import RefRed.colors
 from RefRed.calculations.add_list_nexus import AddListNexus
-from RefRed.calculations.lr_data import LRData
 from RefRed.calculations.locate_list_run import LocateListRun
-from RefRed.calculations.update_reduction_table_metadata import UpdateReductionTableMetadata
+from RefRed.calculations.lr_data import LRData
+from RefRed.calculations.update_reduction_table_metadata import (
+    UpdateReductionTableMetadata,
+)
+from RefRed.gui_handling.gui_utility import GuiUtility
 from RefRed.gui_handling.progressbar_handler import ProgressBarHandler
 from RefRed.plot.display_plots import DisplayPlots
-from RefRed.gui_handling.gui_utility import GuiUtility
-import RefRed.colors
 
 
 class LoadReductionTableFromLConfigDataSet(object):
@@ -29,7 +32,7 @@ def __init__(self, parent=None):
             list_data_run = lconfig.data_sets
             o_list_data_nexus = LocateListRun(list_run=list_data_run)
             list_data_nexus = o_list_data_nexus.list_nexus_found
-            #            list_data_nexus= o_list_data_nexus.list_run_found
+            # list_data_nexus= o_list_data_nexus.list_run_found
             _add_data_nexus = AddListNexus(
                 list_nexus=list_data_nexus,
                 list_run=list_data_run,

RefRed/configuration/loading_configuration.py

@@ -56,7 +56,8 @@ def run(self):
                 try:
                     self.loading()
                     message = "Done!"
-                except:
+                except Exception as e:
+                    logging.error(f"Error loading file: {e}")
                     message = "Error loading file: aborted"
             else:
                 message = "Loading aborted"
@@ -187,6 +188,12 @@ def populate_main_gui_general_settings(self):
         self.parent.deadtime_settings.from_xml(node_0)
         self.parent.ui.deadtime_entry.applyCheckBox.setChecked(self.parent.deadtime_settings.apply_deadtime)
 
+        # initialize the instrument settings
+        self.parent.instrument_settings.from_xml(node_0)
+        self.parent.ui.instrument_settings_entry.applyCheckBox.setChecked(
+            self.parent.instrument_settings.apply_instrument_settings
+        )
+
     def getMetadataObject(self, node) -> LConfigDataset:
         r"""Populate an instance of type LConfigDataset using the information contained in one of the
         'RefLData    XML blocks within a configuration file."""

RefRed/configuration/saving_configuration.py

@@ -17,6 +17,7 @@ def __init__(self, parent=None, filename=''):
         StatusMessageHandler(parent=self.parent, message='Saving config ...', is_threaded=False)
 
     def run(self):
+
         if self.filename == '':
             _path = self.parent.path_config
             _filter = "XML (*.xml);; All Files (*.*)"

RefRed/interfaces/deadtime_entry.py

@@ -1,9 +1,8 @@
-# third party imports
 from qtpy.QtWidgets import QGroupBox, QHBoxLayout, QCheckBox, QPushButton
 
 
 class DeadTimeEntryPoint(QGroupBox):
-    def __init__(self, title='Dead Time Correction'):
+    def __init__(self, title="Dead Time Correction"):
         super().__init__(title)
         self.initUI()
 
@@ -22,16 +21,19 @@ def initUI(self):
             "}"
         )
 
-        self.applyCheckBox = QCheckBox('Apply', self)
+        self.applyCheckBox = QCheckBox("Apply", self)
         self.applyCheckBox.stateChanged.connect(self.toggleSettingsButton)
-        self.settingsButton = QPushButton('Settings', self)
-        self.settingsButton.setEnabled(self.applyCheckBox.isChecked())  # enabled if we use the correction
+        self.settingsButton = QPushButton("Settings", self)
+        self.settingsButton.setEnabled(
+            # enabled if we use the correction
+            self.applyCheckBox.isChecked()
+        )
 
         # Create a horizontal layout for the checkbox and settings button
         hbox = QHBoxLayout()
         hbox.addWidget(self.applyCheckBox)
         hbox.addWidget(self.settingsButton)
-        hbox.addStretch(1)  # This adds a stretchable space after the button (optional)
+        # hbox.addStretch(1)  # This adds a stretchable space after the button (optional)
 
         # Set the layout for the group box
         self.setLayout(hbox)